Guillaume Delevoye's repositories
cigarfilter
A fast C++ tool to filter .bam files by CIGAR string
kmers_removal
Small example of how a list of kmers can be removed from a genome assembly
bamtools
C++ API & command-line toolkit for working with BAM data
bedops
:microscope: BEDOPS: high-performance genomic feature operations
cmake-conan
CMake wrapper for conan C and C++ package manager
elixir-workshop-21
Nextflow workflow workshop 2021
entt
Gaming meets modern C++ - a fast and reliable entity component system (ECS) and much more
Example-.bam-filter-C-
Minimal example to filter .bam files in C++
genozip
A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
glsmac
Open-source SMAC (Sid Meier's Alpha Centauri) engine
gWQS
:exclamation: This is a read-only mirror of the CRAN R package repository. gWQS — Generalized Weighted Quantile Sum Regression
imgui_markdown
Markdown for Dear ImGui
implot
Immediate Mode Plotting
methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
mgzip
A multi-threading implement of Python gzip module
pandarallel
A simple and efficient tool to parallelize Pandas operations on all available CPUs
pbbam
PacBio BAM C++ library
pcawg3-rnaseq-align-star
Scripts for RNA-Seq alignments using STAR
plink-ng
A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.
pyComBat
pyComBat is a Python 3 implementation of ComBat, one of the most widely used tool for correcting technical biases, called batch effects, in microarray expression data.
revelio
A lightweight utility for BS-seq and MethylC-seq data which applies a double-masking procedure on bisulfite alignments, facilitating variant calling with conventional software.
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
SFML
Simple and Fast Multimedia Library
snp
The EpiDiverse Bisulfite SNP-Calling and Methylation Clustering Pipeline, implemented with Nextflow
ThreadPool
A simple C++11 Thread Pool implementation